[English] 日本語
Yorodumi
- PDB-8bs9: Structure of USP36 in complex with Ubiquitin-PA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bs9
TitleStructure of USP36 in complex with Ubiquitin-PA
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 36
KeywordsHYDROLASE / USP / USP36 / Ubiquitin / Fubi / S30 / Fau / probe / DUB / DUBs / Deubiquitinase
Function / homology
Function and homology information


histone H2B deubiquitinase activity / regulation of rRNA processing / regulation of mitophagy / nucleolus organization / Transferases; Acyltransferases; Aminoacyltransferases / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked deubiquitinase activity / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of protein targeting to mitochondrion ...histone H2B deubiquitinase activity / regulation of rRNA processing / regulation of mitophagy / nucleolus organization / Transferases; Acyltransferases; Aminoacyltransferases / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked deubiquitinase activity / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of protein targeting to mitochondrion / fat pad development / mitochondrion transport along microtubule / negative regulation of macroautophagy / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / : ...: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsO'Dea, R. / Gersch, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck SocietyCGC-III-352S Germany
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Molecular basis for ubiquitin/Fubi cross-reactivity in USP16 and USP36.
Authors: O'Dea, R. / Kazi, N. / Hoffmann-Benito, A. / Zhao, Z. / Recknagel, S. / Wendrich, K. / Janning, P. / Gersch, M.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 15, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 36
B: Polyubiquitin-B
C: Ubiquitin carboxyl-terminal hydrolase 36
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,52712
Polymers95,1054
Non-polymers4228
Water12,088671
1
A: Ubiquitin carboxyl-terminal hydrolase 36
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7646
Polymers47,5532
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-19 kcal/mol
Surface area16130 Å2
MethodPISA
2
C: Ubiquitin carboxyl-terminal hydrolase 36
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7646
Polymers47,5532
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-16 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.743, 65.307, 103.411
Angle α, β, γ (deg.)90.000, 93.265, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Ubiquitin carboxyl-terminal hydrolase 36 / Deubiquitinating enzyme 36 / Ubiquitin thioesterase 36 / Ubiquitin-specific-processing protease 36


Mass: 39032.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP36, KIAA1453 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P275, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

-
Non-polymers , 4 types, 679 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.3 M potassium formate, 14% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 1.9→45.24 Å / Num. obs: 152836 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 15177 / CC1/2: 0.604 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSVERSION Jan 10, 2022 BUILT=20220110data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.24 Å / SU ML: 0.2379 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 7607 4.98 %
Rwork0.171 145146 -
obs0.173 152753 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6170 0 14 671 6855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046326
X-RAY DIFFRACTIONf_angle_d1.00698586
X-RAY DIFFRACTIONf_chiral_restr0.0644978
X-RAY DIFFRACTIONf_plane_restr0.00871107
X-RAY DIFFRACTIONf_dihedral_angle_d14.59822261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.32592800.32784852X-RAY DIFFRACTION97.03
1.92-1.940.36662700.31584725X-RAY DIFFRACTION97.79
1.94-1.970.34451980.34849X-RAY DIFFRACTION97.17
1.97-1.990.29372140.29044911X-RAY DIFFRACTION97.75
1.99-2.020.30182670.27344754X-RAY DIFFRACTION97.89
2.02-2.050.29692320.264951X-RAY DIFFRACTION97.68
2.05-2.080.27822390.2434802X-RAY DIFFRACTION98.04
2.08-2.110.30032420.2424877X-RAY DIFFRACTION97.21
2.11-2.140.28022680.23114741X-RAY DIFFRACTION98.23
2.14-2.170.27482700.22344871X-RAY DIFFRACTION97.44
2.17-2.210.25522500.21214744X-RAY DIFFRACTION97.1
2.21-2.250.25022820.20394746X-RAY DIFFRACTION96.9
2.25-2.30.27882780.2024841X-RAY DIFFRACTION97.86
2.3-2.340.23642370.18474891X-RAY DIFFRACTION98.22
2.34-2.390.23742360.18714864X-RAY DIFFRACTION98.95
2.39-2.450.24572480.17774902X-RAY DIFFRACTION98.36
2.45-2.510.22452850.17734844X-RAY DIFFRACTION98.46
2.51-2.580.18472210.17664896X-RAY DIFFRACTION98.94
2.58-2.650.22092680.17724837X-RAY DIFFRACTION98.1
2.65-2.740.21612740.17914799X-RAY DIFFRACTION98.64
2.74-2.840.22733090.16584878X-RAY DIFFRACTION98.82
2.84-2.950.21172780.16134865X-RAY DIFFRACTION98.75
2.95-3.090.21752430.15794804X-RAY DIFFRACTION97.77
3.09-3.250.19642660.15474776X-RAY DIFFRACTION96.68
3.25-3.450.17792410.15214897X-RAY DIFFRACTION98.54
3.45-3.720.16732660.13834835X-RAY DIFFRACTION98.78
3.72-4.090.15342770.13294846X-RAY DIFFRACTION98.46
4.09-4.680.18432210.12124888X-RAY DIFFRACTION98.19
4.68-5.90.19132260.14744847X-RAY DIFFRACTION97.41
5.9-45.240.17542210.17774813X-RAY DIFFRACTION97.03

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more